AI × Biology · Whole-cell models · Agentic ML

Portrait of Evangelos-Marios Nikolados

I'm Head of AI at Myria Biosciences, where AI-designed microbes produce macrocyclic-peptide therapeutics. I lead the machine-learning and data platforms that turn the company's discovery and design data into decisions.

I build the models and platforms that make living cells predictable — and, ultimately, programmable.

More broadly, my work spans the two halves of biological modelling that rarely meet: mechanistic, mathematical models of how cells work — whole-cell simulation, dynamical systems, resource allocation — and machine learning that predicts biological function directly from sequence and data. I believe the next advance in AI-for-biology comes from fusing the two, wrapped in autonomous agents that design and run their own experiments — toward an AI-driven virtual cell you can query, steer, and trust.

Previously I earned my PhD at the University of Edinburgh (deep learning for protein expression), with earlier degrees from Imperial College London and Harvard.

GitHub activity

GitHub contributions calendar GitHub contributions calendar

News

2024 Completed my PhD in Quantitative Biology at the University of Edinburgh.

Selected work independent of my role at Myria

seq2yield-agent In development github.com/evanniko1/seq2yield-agent

A self-driving ML system that automatically builds, critiques, and improves models predicting expression or yield from short biological sequences — for any such dataset, not one hand-tuned model. An LLM council proposes approaches, reviewers challenge them, and a bounded ML-engineer loop validates each under fixed metrics. Already spans five public datasets (~1.12M sequences across E. coli, yeast, and human).

wcEcoli Platform & Coli Agent In development github.com/MohammedNagdi/wcEcoli/tree/feature/wcecoli-platform

A platform that opens a molecular-resolution whole-cell E. coli model (~1,592 genes) to a natural-language agent: design knockout and media-shift experiments, launch batch simulations, and analyse results by conversation, with human approval for any state change — putting whole-cell modelling in the hands of experimental biologists and students, not just computational specialists.

The Well, for the Cell In development

A public ML benchmark of whole-cell dynamics — the biology counterpart to Polymathic AI's The Well. A large, standardized corpus of whole-cell E. coli simulation trajectories (fully observable, causally perturbed, dynamic) with benchmark tasks, leakage-free splits, and baselines: model-derived data that complements the sparse, noisy snapshots of experimental omics. The wcEcoli platform generates the corpus; the Coli agent is its grounded query interface.

Cellarium Hackathon · 2026 github.com/evanniko1/cellarium

A grounded, guardrailed Claude copilot over a whole-cell E. coli simulation, built for the Built with Claude: Life Sciences hackathon. It answers only from real simulation data and enforces biosecurity and scientific guardrails — refusing experiments outside the model's validated envelope and withholding non-viable results rather than laundering them into clean-looking numbers.

Contact

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